Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_012040872.1 BBTA_RS02575 dihydroxy-acid dehydratase
Query= curated2:B5YKD5 (550 letters) >NCBI__GCF_000015165.1:WP_012040872.1 Length = 578 Score = 356 bits (914), Expect = e-102 Identities = 200/539 (37%), Positives = 319/539 (59%), Gaps = 13/539 (2%) Query: 15 HRALLFATGIPKSEMN-KPFIGVATSFTDIIPGHISMKELERFIEKGIHTGGGYPFFFGI 73 HR+ + G + E +P I + +++D P H+ K+ +++G+ GG+P Sbjct: 26 HRSRVMQMGYAQEEWKGRPVIAIVNTWSDAQPCHMHFKQRVDDVKRGVLMAGGFPIELPA 85 Query: 74 PGICDGIAMGHKGMKYSLPSRELIADIIECIVEAHQFDGIVLLTNCDKITPGMLMAAARL 133 + + + + M Y R ++A +E ++ +H DG+VL+ CDK TP +L+ A + Sbjct: 86 LSLSESL-LKPTTMLY----RNMLAMDVEELLRSHPVDGVVLMGGCDKTTPALLLGATSM 140 Query: 134 DIPAIVLTAGPMLAGYYKGQRRNLTSDTFEAIGKFKKGVLTEKDLEALELCACPGAGSCQ 193 ++PAI L AGPML G +KG+ SD ++ + + G L++ D A+E G+C Sbjct: 141 NLPAIYLPAGPMLRGNWKGKTLGSGSDAWKYWDERRAGKLSDADWSAMEAGIARSHGTCM 200 Query: 194 GMYTANTMACVTEALGMSLPGTAATPAVMSEKRRLAFETGVKIVELVRKKINARQILTKE 253 M TA+TM + EA+GM+LPG ++ PA +E R++ E G +IVE+V + + +I +++ Sbjct: 201 TMGTASTMTAIAEAIGMTLPGASSIPAADAEHIRMSSECGRRIVEMVWEDLTPAKIQSRQ 260 Query: 254 AFYNAIAVDMALGGSTNTVLHIKAIANEAGINLPLEVFDEISRKTPHLVNIIPSGEHY-M 312 AF NAIAV MA+G STN ++H+ A A AG ++ L+ F+ SRK P L N+ PSG+ Y M Sbjct: 261 AFENAIAVAMAMGCSTNAIIHVIAQARRAGADIGLDDFEAASRKVPVLANVRPSGDTYLM 320 Query: 313 EDLYKAGGIPAVLKRLKDKIYSN-PTVSGIDIKEIAQKAEIYDENVIRSIKKAYHKEGGV 371 ED Y AGG+P ++ R+K+ ++ TV+G + + A +Y+++VIR ++EG + Sbjct: 321 EDFYYAGGLPGLMSRMKEHLHLGCLTVNGRTLGDNIADAGVYNDDVIRPQSNPIYREGAL 380 Query: 372 AILKGNLAPDGAVVKQTAVSSKMLKFEGIARCFDSEENAMKAILDG--KIKEGDVIIIRY 429 A+LKGNLAPDG V+K +A + LK G A FD + KAI D + V+I+R Sbjct: 381 AVLKGNLAPDGCVIKPSACDPRFLKHTGPALVFDDYPSMKKAIDDPDLDVTADHVLILRN 440 Query: 430 EGPSGGPGMRE--MLSPTSAITGMGLNESVALITDGRFSGGTRGPCIGHVSPEAARGGPI 487 GP GGPGM E ML + + G+ + V L +D R SG + G CI HV+PEA GGP+ Sbjct: 441 AGPQGGPGMPEWGMLPIPTKLVKQGVRDMVRL-SDARMSGTSYGACILHVAPEAYVGGPL 499 Query: 488 AIVKDGDKILIDIPKRKIEILISESEIKKRLKNWKPPKQKIEKGYLLRYARNVSSADKG 546 A+V++GD I +D+ R I++ + E E+ +R W+PP + E+GY +AR++ A+ G Sbjct: 500 ALVRNGDLITLDVAARTIDLDVPEDELARRRAEWQPPAPRFERGYGWMFARHIKQANDG 558 Lambda K H 0.318 0.137 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 756 Number of extensions: 37 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 550 Length of database: 578 Length adjustment: 36 Effective length of query: 514 Effective length of database: 542 Effective search space: 278588 Effective search space used: 278588 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory